<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<title>MolTK C++ API: moltk::BaseBiosequence Class Reference</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>
<link href="doxygen.css" rel="stylesheet" type="text/css" />

<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
  $(document).ready(function() { searchBox.OnSelectItem(0); });
</script>

</head>
<body>
<div id="top"><!-- do not remove this div! -->


<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  
  <td id="projectlogo"><img alt="Logo" src="moltk55.png"/></td>
  
  
  <td style="padding-left: 0.5em;">
   <div id="projectname">MolTK C++ API
   &#160;<span id="projectnumber">0.4.0</span>
   </div>
   
  </td>
  
  
  
 </tr>
 </tbody>
</table>
</div>

<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
  <div id="navrow1" class="tabs">
    <ul class="tablist">
      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
      <li><a href="files.html"><span>Files</span></a></li>
      <li>
        <div id="MSearchBox" class="MSearchBoxInactive">
        <span class="left">
          <img id="MSearchSelect" src="search/mag_sel.png"
               onmouseover="return searchBox.OnSearchSelectShow()"
               onmouseout="return searchBox.OnSearchSelectHide()"
               alt=""/>
          <input type="text" id="MSearchField" value="Search" accesskey="S"
               onfocus="searchBox.OnSearchFieldFocus(true)" 
               onblur="searchBox.OnSearchFieldFocus(false)" 
               onkeyup="searchBox.OnSearchFieldChange(event)"/>
          </span><span class="right">
            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
          </span>
        </div>
      </li>
    </ul>
  </div>
  <div id="navrow2" class="tabs2">
    <ul class="tablist">
      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
      <li><a href="inherits.html"><span>Class&#160;Hierarchy</span></a></li>
      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
    </ul>
  </div>
  <div id="nav-path" class="navpath">
    <ul>
      <li class="navelem"><a class="el" href="namespacemoltk.html">moltk</a>      </li>
      <li class="navelem"><a class="el" href="classmoltk_1_1BaseBiosequence.html">BaseBiosequence</a>      </li>
    </ul>
  </div>
</div>
<div class="header">
  <div class="summary">
<a href="#nested-classes">Classes</a> &#124;
<a href="#pub-methods">Public Member Functions</a>  </div>
  <div class="headertitle">
<div class="title">moltk::BaseBiosequence Class Reference</div>  </div>
</div>
<div class="contents">
<!-- doxytag: class="moltk::BaseBiosequence" -->
<p>Parent class for macromolecule sequences and structures.  
 <a href="classmoltk_1_1BaseBiosequence.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="Biosequence_8hpp_source.html">Biosequence.hpp</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for moltk::BaseBiosequence:</div>
<div class="dyncontent">
<div class="center"><img src="classmoltk_1_1BaseBiosequence__inherit__graph.png" border="0" usemap="#moltk_1_1BaseBiosequence_inherit__map" alt="Inheritance graph"/></div>
<map name="moltk_1_1BaseBiosequence_inherit__map" id="moltk_1_1BaseBiosequence_inherit__map">
<area shape="rect" id="node3" href="classmoltk_1_1Biosequence.html" title="A macromolecule sequence (DNA or RNA or protein)" alt="" coords="5,80,141,107"/><area shape="rect" id="node5" href="classmoltk_1_1PDBStructure_1_1Chain.html" title="Chain represents a single polymer or molecule in a PDBStructure." alt="" coords="166,80,348,107"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>

<p><a href="classmoltk_1_1BaseBiosequence-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">BaseResidue</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Parent class for macromolecule sequence residues (nucleotides or amino acids)  <a href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseBiosequence.html#ab40016d2526566c4dc17b29eaeb3dc74">BaseBiosequence</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseBiosequence.html#a50d0c5d8f88038a316eb2cf1a4a8cb54">~BaseBiosequence</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseBiosequence.html#aab2f57949c05883dc8ca85577d634f4d">write_to_stream</a> (std::ostream &amp;os) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseBiosequence.html#a837f45a8604c435855b00aa90ace5841">get_number_of_residues</a> () const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual const <a class="el" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">BaseResidue</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1BaseBiosequence.html#ae966c9bf162db00c2d5a4898170538af">get_residue</a> (size_t index) const =0</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Parent class for macromolecule sequences and structures. </p>
</div><hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="ab40016d2526566c4dc17b29eaeb3dc74"></a><!-- doxytag: member="moltk::BaseBiosequence::BaseBiosequence" ref="ab40016d2526566c4dc17b29eaeb3dc74" args="()" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">moltk::BaseBiosequence::BaseBiosequence </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a50d0c5d8f88038a316eb2cf1a4a8cb54"></a><!-- doxytag: member="moltk::BaseBiosequence::~BaseBiosequence" ref="a50d0c5d8f88038a316eb2cf1a4a8cb54" args="()" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">virtual moltk::BaseBiosequence::~BaseBiosequence </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline, virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a837f45a8604c435855b00aa90ace5841"></a><!-- doxytag: member="moltk::BaseBiosequence::get_number_of_residues" ref="a837f45a8604c435855b00aa90ace5841" args="() const =0" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">virtual size_t moltk::BaseBiosequence::get_number_of_residues </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implemented in <a class="el" href="classmoltk_1_1Biosequence.html#ac990688fe005304a3dd512a616017c71">moltk::Biosequence</a>, and <a class="el" href="classmoltk_1_1PDBStructure_1_1Chain.html#acbde49bcc732f9830a3c1d60e37c0644">moltk::PDBStructure::Chain</a>.</p>

</div>
</div>
<a class="anchor" id="ae966c9bf162db00c2d5a4898170538af"></a><!-- doxytag: member="moltk::BaseBiosequence::get_residue" ref="ae966c9bf162db00c2d5a4898170538af" args="(size_t index) const =0" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">virtual const <a class="el" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html">BaseResidue</a>&amp; moltk::BaseBiosequence::get_residue </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>index</em></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implemented in <a class="el" href="classmoltk_1_1Biosequence.html#a7347126c11c30536dfc3b0214f0dcc44">moltk::Biosequence</a>, and <a class="el" href="classmoltk_1_1PDBStructure_1_1Chain.html#a24980b95a88bb1476c283a6f91944a2c">moltk::PDBStructure::Chain</a>.</p>

</div>
</div>
<a class="anchor" id="aab2f57949c05883dc8ca85577d634f4d"></a><!-- doxytag: member="moltk::BaseBiosequence::write_to_stream" ref="aab2f57949c05883dc8ca85577d634f4d" args="(std::ostream &amp;os) const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">virtual void moltk::BaseBiosequence::write_to_stream </td>
          <td>(</td>
          <td class="paramtype">std::ostream &amp;&#160;</td>
          <td class="paramname"><em>os</em></td><td>)</td>
          <td> const<code> [virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="Biosequence_8hpp_source.html">Biosequence.hpp</a></li>
</ul>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Friends</a></div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>



<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.7.5.1
</small></address>

</body>
</html>
